Hi,
I do not think that what Per suggests is the problem, if you look at the
potential energy after the minimisation this value is huge (and the other
two values are inf!). The problem is most likely with your topology. As you
say the two molecules have been successfully minimised on their own so I
would suggest that your problem is with either how you edit the .top file
or the distance restraint between the molecules. For my protein that has
more than one identical chains pdb2gmx does not recognise them as one if
you provide different chain identifiers in the pdb file, so doing this
should hopefully stop you having to edit the .top file.
Hope this helps
Tom
--On 17 August 2007 19:02 +0200 Per Larsson <[EMAIL PROTECTED]> wrote:
Hello!
Check out
http://wiki.gromacs.org/index.php/Errors#Stepsize_too_small.2C_or_no_chan
ge_in_energy._Converged_to_machine_precision.2C_but_not_to_the_requested_
precision
Cheers
/Per
17 aug 2007 kl. 18.28 skrev Sheyore Omovie:
Dear gmx-users,
I have 2 molecules in a box, as usual pdb2gmx saw them as one. i edited
the .top file to remove the bonds created between the two molecules, I
also added a distance restraint btw the molecules. (The 2 structures have
been separately minimized). However, I get the ff message for EM run:
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1000
Double precision normally gives you higher accuracy.
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 1000.
Potential Energy = 1.0246325e+20
Maximum force = inf on atom 1
Norm of force = inf I would appreciate any advice on how
to fix this.
Rgds
John
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TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
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